Genome Sequence of the Edible Green Alga Ulva prolifera, Originating from the Yoshinogawa River in Japan

ABSTRACT We report the genome sequence of Ulva prolifera, which originated from the Yoshinogawa River in Japan, using Oxford Nanopore Technologies MinION and Illumina sequencing reads. The genome assembly size is 103.8 Mbp, consisting of 142 scaffolds with an N50 value of 4.11 Mbp.

U lva prolifera (Sujiaonori in Japanese) is one of the most important edible green alga in Japan. It grows in brackish river mouths; however, natural populations of U. prolifera in Japan have been decreasing, and a tank cultivation system has been developed for sustainable production (1). U. prolifera is also one of the sources of troublesome green tide (2). The genome sequence of U. prolifera collected from the Yellow Sea was recently reported (3); however, it is known that brackish strains and bloom-forming marine habitat strains show different characteristics, and new subspecies for the latter strains have been proposed (4,5).
An U. prolifera sample for genome sequencing was collected from a land culture at Hashirijima Island (Hiroshima, Japan) that was originally derived from the Yoshinogawa River (Tokushima, Japan). The thallus, with a length of .20 cm, was cut into small pieces, frozen in liquid nitrogen, and finely powdered using a Micro Smash MS-100 cell disruptor (Tomy Seiko). Genomic DNA (gDNA) was extracted using the NucleoBond high-molecularweight (HMW) DNA kit (Macherey-Nagel), and we did not perform either DNA shearing or size selection. A Nanopore sequencing library was prepared from 1 mg of gDNA using a ligation sequencing kit (SQK-LSK110; Oxford Nanopore Technologies [ONT]). Nanopore sequencing was performed on an ONT MinION sequencer using a R9.4.1 flow cell (FLO-MIN106D). One-half volume of the library was sequenced for 24 h, and the other one-half volume of the library was sequenced for 22 h after a flow cell wash step. The raw FAST5 files obtained for the two sequencing runs were base called using Guppy v6.0.1 (ONT) with a high-accuracy model ( Table 1). An Illumina sequencing library was prepared using the NEBNext Ultra DNA library preparation kit for Illumina (New England Biolabs) and sequenced on an Illumina NovaSeq 6000 system in the 150-bp paired-end mode ( Table 1).
Data availability. This whole-genome shotgun project has been deposited in DDBJ under the accession numbers BRCE01000001 to BRCE01000142. The raw Nanopore and Illumina reads have been deposited in DDBJ under the accession numbers DRR361634 and DRR361635, respectively. Additional information on the parameter settings and draft assembly results with tested assemblers can be found at figshare (https://doi.org/10.6084/ m9.figshare.19728862).

ACKNOWLEDGMENTS
We thank Mishima Foods Co., Ltd., for providing a sample of U. prolifera for genome sequencing.
This work was supported by the Center of Innovation for Bio-Digital Transformation (BioDX), a Japan Science and Technology Agency (JST) open innovation platform for industryacademia cocreation (COI-NEXT) (grant JPMJPF2010). Computations were partially performed on the supercomputer at the ROIS National Institute of Genetics.